Custom Blender Builds: How do they work together?
In short: until both features are merged into the same build of Blender, you should treat those Blenders as two different applications.

I would suggest to use a file format like Alembic to bridge the different applications you want to use. For example, use the Fracture build of Blender to produce fractured objects, then export those to Alembic. You can then use the Manta Flow build of Blender to import those Alembic files and work with MantaFlow.